C# IAtomContainer.getConnectedAtomsVector方法代码示例

 /// <summary>  Return the neighbours of atom <code>a</code> in canonical order with the
 /// atoms that have high bond order at the front.
 /// 
 /// </summary>
 /// <param name="a">         the atom whose neighbours are to be found.
 /// </param>
 /// <param name="container"> the AtomContainer that is being parsed.
 /// </param>
 /// <returns>            Vector of atoms in canonical oreder.
 /// </returns>
 private System.Collections.IList getCanNeigh(IAtom a, IAtomContainer container)
 {
     System.Collections.IList v = container.getConnectedAtomsVector(a);
     if (v.Count > 1)
     {
         SupportClass.CollectionsSupport.Sort(v, new AnonymousClassComparator(this));
     }
     return v;
 }

        /// <summary>  Parse a branch
        /// 
        /// </summary>
        /// <param name="v">                       Description of Parameter
        /// </param>
        /// <param name="buffer">                  Description of Parameter
        /// </param>
        /// <param name="container">               Description of Parameter
        /// </param>
        /// <param name="parent">                  Description of Parameter
        /// </param>
        /// <param name="chiral">                  Description of Parameter
        /// </param>
        /// <param name="doubleBondConfiguration"> Description of Parameter
        /// </param>
        /// <param name="atomsInOrderOfSmiles">    Description of Parameter
        /// </param>
        private void parseChain(System.Collections.ArrayList v, System.Text.StringBuilder buffer, IAtomContainer container, IAtom parent, bool chiral, bool[] doubleBondConfiguration, System.Collections.ArrayList atomsInOrderOfSmiles)
        {
            int positionInVector = 0;
            IAtom atom;
            //System.out.println("in parse chain. Size of tree: " + v.size());
            for (int h = 0; h < v.Count; h++)
            {
                System.Object o = v[h];
                if (o is IAtom)
                {
                    atom = (IAtom)o;
                    if (parent != null)
                    {
                        parseBond(buffer, atom, parent, container);
                    }
                    else
                    {
                        if (chiral && BondTools.isStereo(container, atom))
                        {
                            parent = (IAtom)((System.Collections.ArrayList)v[1])[0];
                        }
                    }
                    parseAtom(atom, buffer, container, chiral, doubleBondConfiguration, parent, atomsInOrderOfSmiles, v);
                    //System.out.println("in parseChain after parseAtom()");
                    /*
                    *  The principle of making chiral smiles is quite simple, although the code is
                    *  pretty uggly. The Atoms connected to the chiral center are put in sorted[] in the
                    *  order they have to appear in the smiles. Then the Vector v is rearranged according
                    *  to sorted[]
                    */
                    if (chiral && BondTools.isStereo(container, atom) && container.getBond(parent, atom) != null)
                    {
                        //System.out.println("in parseChain in isChiral");
                        IAtom[] sorted = null;
                        System.Collections.IList chiralNeighbours = container.getConnectedAtomsVector(atom);
                        if (BondTools.isTetrahedral(container, atom, false) > 0)
                        {
                            sorted = new IAtom[3];
                        }
                        if (BondTools.isTetrahedral(container, atom, false) == 1)
                        {
                            if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_DOWN)
                            {
                                for (int i = 0; i < chiralNeighbours.Count; i++)
                                {
                                    if (chiralNeighbours[i] != parent)
                                    {
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[2] = (IAtom)chiralNeighbours[i];
                                        }
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[1] = (IAtom)chiralNeighbours[i];
                                        }
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_UP && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[0] = (IAtom)chiralNeighbours[i];
                                        }
                                    }
                                }
                            }
                            if (container.getBond(parent, atom).Stereo == CDKConstants.STEREO_BOND_UP)
                            {
                                for (int i = 0; i < chiralNeighbours.Count; i++)
                                {
                                    if (chiralNeighbours[i] != parent)
                                    {
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[1] = (IAtom)chiralNeighbours[i];
                                        }
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == 0 && !BondTools.isLeft(((IAtom)chiralNeighbours[i]), parent, atom) && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[2] = (IAtom)chiralNeighbours[i];
                                        }
                                        if (container.getBond((IAtom)chiralNeighbours[i], atom).Stereo == CDKConstants.STEREO_BOND_DOWN && !isBondBroken((IAtom)chiralNeighbours[i], atom))
                                        {
                                            sorted[0] = (IAtom)chiralNeighbours[i];
                                        }
                                    }
                                }
                            }
//.........这里部分代码省略.........

 /// <summary> Calculates the product of the neighbouring primes.
 /// 
 /// </summary>
 /// <param name="v">the invariance pair vector
 /// </param>
 private void primeProduct(System.Collections.ArrayList v, IAtomContainer atomContainer)
 {
     System.Collections.IEnumerator it = v.GetEnumerator();
     System.Collections.IEnumerator n;
     InvPair inv;
     IAtom a;
     long summ;
     //UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
     while (it.MoveNext())
     {
         //UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
         inv = (InvPair)it.Current;
         System.Collections.IList neighbour = atomContainer.getConnectedAtomsVector(inv.Atom);
         n = neighbour.GetEnumerator();
         summ = 1;
         //UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
         while (n.MoveNext())
         {
             //UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
             a = (IAtom)n.Current;
             int next = ((InvPair)a.getProperty(InvPair.INVARIANCE_PAIR)).getPrime();
             summ = summ * next;
         }
         inv.Last = inv.Curr;
         inv.Curr = summ;
     }
 }

 /// <summary> Get the paths starting from an atom of specified length.
 /// <p/>
 /// This method returns a set of paths. Each path is a <code>List</code> of atoms that
 /// make up the path (ie they are sequentially connected).
 /// 
 /// </summary>
 /// <param name="atomContainer">The molecule to consider
 /// </param>
 /// <param name="start">        The starting atom
 /// </param>
 /// <param name="length">       The length of paths to look for
 /// </param>
 /// <returns> A  <code>List</code> containing the paths found
 /// </returns>
 public static System.Collections.IList getPathsOfLength(IAtomContainer atomContainer, IAtom start, int length)
 {
     System.Collections.ArrayList curPath = new System.Collections.ArrayList();
     System.Collections.ArrayList paths = new System.Collections.ArrayList();
     curPath.Add(start);
     paths.Add(curPath);
     for (int i = 0; i < length; i++)
     {
         System.Collections.ArrayList tmpList = new System.Collections.ArrayList();
         for (int j = 0; j < paths.Count; j++)
         {
             curPath = (System.Collections.ArrayList)paths[j];
             IAtom lastVertex = (IAtom)curPath[curPath.Count - 1];
             System.Collections.IList neighbors = atomContainer.getConnectedAtomsVector(lastVertex);
             for (int k = 0; k < neighbors.Count; k++)
             {
                 System.Collections.ArrayList newPath = new System.Collections.ArrayList(curPath);
                 if (newPath.Contains(neighbors[k]))
                     continue;
                 newPath.Add(neighbors[k]);
                 tmpList.Add(newPath);
             }
         }
         paths.Clear();
         paths.AddRange(tmpList);
     }
     return (paths);
 }

 private static void findPathBetween(IAtomContainer atomContainer, IAtom start, IAtom end, System.Collections.IList path)
 {
     if (start == end)
     {
         path.Add(start);
         allPaths.Add(new System.Collections.ArrayList(path));
         path.RemoveAt(path.Count - 1);
         return;
     }
     if (path.Contains(start))
         return;
     path.Add(start);
     System.Collections.IList nbrs = atomContainer.getConnectedAtomsVector(start);
     //UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
     for (System.Collections.IEnumerator i = nbrs.GetEnumerator(); i.MoveNext(); )
     {
         //UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
         findPathBetween(atomContainer, (IAtom)i.Current, end, path);
     }
     path.RemoveAt(path.Count - 1);
 }

 /// <summary>  Says if of four atoms connected two one atom the up and down bonds are
 /// opposite or not, i. e.if it's tetrehedral or square planar. The method
 /// doesnot check if there are four atoms and if two or up and two are down
 /// 
 /// </summary>
 /// <param name="a">         The atom which is the center
 /// </param>
 /// <param name="container"> The atomContainer the atom is in
 /// </param>
 /// <returns>            true=are opposite, false=are not
 /// </returns>
 public static bool stereosAreOpposite(IAtomContainer container, IAtom a)
 {
     System.Collections.IList atoms = container.getConnectedAtomsVector(a);
     //UPGRADE_ISSUE: Class hierarchy differences between 'java.util.TreeMap' and 'System.Collections.SortedList' may cause compilation errors. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1186'"
     //UPGRADE_TODO: Constructor 'java.util.TreeMap.TreeMap' was converted to 'System.Collections.SortedList' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapTreeMap'"
     System.Collections.SortedList hm = new System.Collections.SortedList();
     for (int i = 1; i < atoms.Count; i++)
     {
         hm[(double)giveAngle(a, (IAtom)atoms[0], ((IAtom)atoms[i]))] = (System.Int32)i;
     }
     //UPGRADE_TODO: Method 'java.util.TreeMap.values' was converted to 'System.Collections.SortedList.Values' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilTreeMapvalues'"
     System.Object[] ohere = SupportClass.ICollectionSupport.ToArray(hm.Values);
     int stereoOne = container.getBond(a, (IAtom)atoms[0]).Stereo;
     int stereoOpposite = container.getBond(a, (IAtom)atoms[(((System.Int32)ohere[1]))]).Stereo;
     if (stereoOpposite == stereoOne)
     {
         return true;
     }
     else
     {
         return false;
     }
 }

        /// <summary> Produces an AtomContainer without explicit Hs but with H count from one with Hs.
        /// The new molecule is a deep copy.
        /// 
        /// </summary>
        /// <param name="atomContainer">The AtomContainer from which to remove the hydrogens
        /// </param>
        /// <returns>              The molecule without Hs.
        /// </returns>
        /// <cdk.keyword>          hydrogen, removal </cdk.keyword>
        public static IAtomContainer removeHydrogens(IAtomContainer atomContainer)
        {
            //UPGRADE_TODO: Class 'java.util.HashMap' was converted to 'System.Collections.Hashtable' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilHashMap'"
            System.Collections.IDictionary map = new System.Collections.Hashtable(); // maps original atoms to clones.
            System.Collections.IList remove = new System.Collections.ArrayList(); // lists removed Hs.

            // Clone atoms except those to be removed.
            IMolecule mol = atomContainer.Builder.newMolecule();
            int count = atomContainer.AtomCount;
            for (int i = 0; i < count; i++)
            {
                // Clone/remove this atom?
                IAtom atom = atomContainer.getAtomAt(i);
                if (!atom.Symbol.Equals("H"))
                {
                    IAtom clonedAtom = null;
                    try
                    {
                        clonedAtom = (IAtom)atom.Clone();
                    }
                    //UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
                    catch (System.Exception e)
                    {
                        // TODO Auto-generated catch block
                        SupportClass.WriteStackTrace(e, Console.Error);
                    }
                    clonedAtom.setHydrogenCount(0);
                    mol.addAtom(clonedAtom);
                    map[atom] = clonedAtom;
                }
                else
                {
                    remove.Add(atom); // maintain list of removed H.
                }
            }

            // Clone bonds except those involving removed atoms.
            count = atomContainer.getBondCount();
            for (int i = 0; i < count; i++)
            {
                // Check bond.
                //UPGRADE_NOTE: Final was removed from the declaration of 'bond '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
                IBond bond = atomContainer.getBondAt(i);
                IAtom[] atoms = bond.getAtoms();
                bool removedBond = false;
                //UPGRADE_NOTE: Final was removed from the declaration of 'length '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
                int length = atoms.Length;
                for (int k = 0; k < length; k++)
                {
                    if (remove.Contains(atoms[k]))
                    {
                        removedBond = true;
                        break;
                    }
                }

                // Clone/remove this bond?
                if (!removedBond)
                // if (!remove.contains(atoms[0]) && !remove.contains(atoms[1]))
                {
                    IBond clone = null;
                    try
                    {
                        clone = (IBond)atomContainer.getBondAt(i).Clone();
                    }
                    //UPGRADE_NOTE: Exception 'java.lang.CloneNotSupportedException' was converted to 'System.Exception' which has different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1100'"
                    catch (System.Exception e)
                    {
                        // TODO Auto-generated catch block
                        SupportClass.WriteStackTrace(e, Console.Error);
                    }
                    clone.setAtoms(new IAtom[] { (IAtom)map[atoms[0]], (IAtom)map[atoms[1]] });
                    mol.addBond(clone);
                }
            }

            // Recompute hydrogen counts of neighbours of removed Hydrogens.
            //UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
            for (System.Collections.IEnumerator i = remove.GetEnumerator(); i.MoveNext(); )
            {
                // Process neighbours.
                //UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
                //UPGRADE_TODO: Method 'java.util.Iterator.hasNext' was converted to 'System.Collections.IEnumerator.MoveNext' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratorhasNext'"
                for (System.Collections.IEnumerator n = atomContainer.getConnectedAtomsVector((IAtom)i.Current).GetEnumerator(); n.MoveNext(); )
                {
                    //UPGRADE_NOTE: Final was removed from the declaration of 'neighb '. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1003'"
                    //UPGRADE_TODO: Method 'java.util.Iterator.next' was converted to 'System.Collections.IEnumerator.Current' which has a different behavior. "ms-help://MS.VSCC.v80/dv_commoner/local/redirect.htm?index='!DefaultContextWindowIndex'&keyword='jlca1073_javautilIteratornext'"
                    IAtom neighb = (IAtom)map[n.Current];
                    neighb.setHydrogenCount(neighb.getHydrogenCount() + 1);
                }
            }
//.........这里部分代码省略.........